Scalable High-Performance Image Registration Framework by Unsupervised Deep Feature Representations Learning

Feature selection is a critical step in deformable image registration. In particular, selecting the most discriminative features that accurately and concisely describe complex morphological patterns in image patches improves correspondence detection, which in turn improves image registration accuracy. Furthermore, since more and more imaging modalities are being invented to better identify morphological changes in medical imaging data,, the development of deformable image registration method that scales well to new image modalities or new image applications with little to no human intervention would have a significant impact on the medical image analysis community. To address these concerns, a learning-based image registration framework is proposed that uses deep learning to discover compact and highly discriminative features upon observed imaging data. Specifically, the proposed feature selection method uses a convolutional stacked auto-encoder to identify intrinsic deep feature representations in image patches. Since deep learning is an unsupervised learning method, no ground truth label knowledge is required. This makes the proposed feature selection method more flexible to new imaging modalities since feature representations can be directly learned from the observed imaging data in a very short amount of time. Using the LONI and ADNI imaging datasets, image registration performance was compared to two existing state-of-the-art deformable image registration methods that use handcrafted features. To demonstrate the scalability of the proposed image registration framework image registration experiments were conducted on 7.0-tesla brain MR images. In all experiments, the results showed the new image registration framework consistently demonstrated more accurate registration results when compared to state-of-the-art

Validação de heterogeneidade estrutural em dados de Crio-ME por comitês de agrupadores

Orientadores: Fernando José Von Zuben, Rodrigo Villares PortugalDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de ComputaçãoResumo: Análise de Partículas Isoladas é uma técnica que permite o estudo da estrutura tridimensional de proteínas e outros complexos macromoleculares de interesse biológico. Seus dados primários consistem em imagens de microscopia eletrônica de transmissão de múltiplas cópias da molécula em orientações aleatórias. Tais imagens são bastante ruidosas devido à baixa dose de elétrons utilizada. Reconstruções 3D podem ser obtidas combinando-se muitas imagens de partículas em orientações similares e estimando seus ângulos relativos. Entretanto, estados conformacionais heterogêneos frequentemente coexistem na amostra, porque os complexos moleculares podem ser flexíveis e também interagir com outras partículas. Heterogeneidade representa um desafio na reconstrução de modelos 3D confiáveis e degrada a resolução dos mesmos. Entre os algoritmos mais populares usados para classificação estrutural estão o agrupamento por k-médias, agrupamento hierárquico, mapas autoorganizáveis e estimadores de máxima verossimilhança. Tais abordagens estão geralmente entrelaçadas à reconstrução dos modelos 3D. No entanto, trabalhos recentes indicam ser possível inferir informações a respeito da estrutura das moléculas diretamente do conjunto de projeções 2D. Dentre estas descobertas, está a relação entre a variabilidade estrutural e manifolds em um espaço de atributos multidimensional. Esta dissertação investiga se um comitê de algoritmos de não-supervisionados é capaz de separar tais "manifolds conformacionais". Métodos de "consenso" tendem a fornecer classificação mais precisa e podem alcançar performance satisfatória em uma ampla gama de conjuntos de dados, se comparados a algoritmos individuais. Nós investigamos o comportamento de seis algoritmos de agrupamento, tanto individualmente quanto combinados em comitês, para a tarefa de classificação de heterogeneidade conformacional. A abordagem proposta foi testada em conjuntos sintéticos e reais contendo misturas de imagens de projeção da proteína Mm-cpn nos estados "aberto" e "fechado". Demonstra-se que comitês de agrupadores podem fornecer informações úteis na validação de particionamentos estruturais independetemente de algoritmos de reconstrução 3DAbstract: Single Particle Analysis is a technique that allows the study of the three-dimensional structure of proteins and other macromolecular assemblies of biological interest. Its primary data consists of transmission electron microscopy images from multiple copies of the molecule in random orientations. Such images are very noisy due to the low electron dose employed. Reconstruction of the macromolecule can be obtained by averaging many images of particles in similar orientations and estimating their relative angles. However, heterogeneous conformational states often co-exist in the sample, because the molecular complexes can be flexible and may also interact with other particles. Heterogeneity poses a challenge to the reconstruction of reliable 3D models and degrades their resolution. Among the most popular algorithms used for structural classification are k-means clustering, hierarchical clustering, self-organizing maps and maximum-likelihood estimators. Such approaches are usually interlaced with the reconstructions of the 3D models. Nevertheless, recent works indicate that it is possible to infer information about the structure of the molecules directly from the dataset of 2D projections. Among these findings is the relationship between structural variability and manifolds in a multidimensional feature space. This dissertation investigates whether an ensemble of unsupervised classification algorithms is able to separate these "conformational manifolds". Ensemble or "consensus" methods tend to provide more accurate classification and may achieve satisfactory performance across a wide range of datasets, when compared with individual algorithms. We investigate the behavior of six clustering algorithms both individually and combined in ensembles for the task of structural heterogeneity classification. The approach was tested on synthetic and real datasets containing a mixture of images from the Mm-cpn chaperonin in the "open" and "closed" states. It is shown that cluster ensembles can provide useful information in validating the structural partitionings independently of 3D reconstruction methodsMestradoEngenharia de ComputaçãoMestre em Engenharia Elétric

CLAIRE: Scalable GPU-Accelerated Algorithms for Diffeomorphic Image Registration in 3D

We present our work on scalable, GPU-accelerated algorithms for diffeomorphic image registration. The associated software package is termed CLAIRE. Image registration is a non-linear inverse problem. It is about computing a spatial mapping from one image of the same object or scene to another. In diffeomorphic image registration, the set of admissible spatial transformations is restricted to maps that are smooth, one-to-one, and have a smooth inverse. We formulate diffeomorphic image registration as a variational problem governed by transport equations. We use an inexact, globalized (Gauss--)Newton--Krylov method for numerical optimization. We consider semi-Lagrangian methods for numerical time integration. Our solver features mixed-precision, hardware-accelerated computational kernels for optimal computational throughput. We use the message-passing interface for distributed-memory parallelism and deploy our code on modern high-performance computing architectures. Our solver allows us to solve clinically relevant problems in under four seconds on a single GPU. It can also be applied to large-scale 3D imaging applications with data that is discretized on meshes with billions of voxels. We demonstrate that our numerical framework yields high-fidelity results in only a few seconds, even if we search for an optimal regularization parameter

Physical Activity Recognition Based on a Parallel Approach for an Ensemble of Machine Learning and Deep Learning Classifiers

Human activity recognition (HAR) by wearable sensor devices embedded in the Internet of things (IOT) can play a significant role in remote health monitoring and emergency notification, to provide healthcare of higher standards. The purpose of this study is to investigate a human activity recognition method of accrued decision accuracy and speed of execution to be applicable in healthcare. This method classifies wearable sensor acceleration time series data of human movement using efficient classifier combination of feature engineering-based and feature learning-based data representation. Leave-one-subject-out cross-validation of the method with data acquired from 44 subjects wearing a single waist-worn accelerometer on a smart textile, and engaged in a variety of 10 activities, yields an average recognition rate of 90%, performing significantly better than individual classifiers. The method easily accommodates functional and computational parallelization to bring execution time significantly down

Nuclei/Cell Detection in Microscopic Skeletal Muscle Fiber Images and Histopathological Brain Tumor Images Using Sparse Optimizations

Nuclei/Cell detection is usually a prerequisite procedure in many computer-aided biomedical image analysis tasks. In this thesis we propose two automatic nuclei/cell detection frameworks. One is for nuclei detection in skeletal muscle fiber images and the other is for brain tumor histopathological images. For skeletal muscle fiber images, the major challenges include: i) shape and size variations of the nuclei, ii) overlapping nuclear clumps, and iii) a series of z-stack images with out-of-focus regions. We propose a novel automatic detection algorithm consisting of the following components: 1) The original z-stack images are first converted into one all-in-focus image. 2) A sufficient number of hypothetical ellipses are then generated for each nuclei contour. 3) Next, a set of representative training samples and discriminative features are selected by a two-stage sparse model. 4) A classifier is trained using the refined training data. 5) Final nuclei detection is obtained by mean-shift clustering based on inner distance. The proposed method was tested on a set of images containing over 1500 nuclei. The results outperform the current state-of-the-art approaches. For brain tumor histopathological images, the major challenges are to handle significant variations in cell appearance and to split touching cells. The proposed novel automatic cell detection consists of: 1) Sparse reconstruction for splitting touching cells. 2) Adaptive dictionary learning for handling cell appearance variations. The proposed method was extensively tested on a data set with over 2000 cells. The result outperforms other state-of-the-art algorithms with F1 score = 0.96

Second-order Temporal Pooling for Action Recognition

Deep learning models for video-based action recognition usually generate features for short clips (consisting of a few frames); such clip-level features are aggregated to video-level representations by computing statistics on these features. Typically zero-th (max) or the first-order (average) statistics are used. In this paper, we explore the benefits of using second-order statistics. Specifically, we propose a novel end-to-end learnable feature aggregation scheme, dubbed temporal correlation pooling that generates an action descriptor for a video sequence by capturing the similarities between the temporal evolution of clip-level CNN features computed across the video. Such a descriptor, while being computationally cheap, also naturally encodes the co-activations of multiple CNN features, thereby providing a richer characterization of actions than their first-order counterparts. We also propose higher-order extensions of this scheme by computing correlations after embedding the CNN features in a reproducing kernel Hilbert space. We provide experiments on benchmark datasets such as HMDB-51 and UCF-101, fine-grained datasets such as MPII Cooking activities and JHMDB, as well as the recent Kinetics-600. Our results demonstrate the advantages of higher-order pooling schemes that when combined with hand-crafted features (as is standard practice) achieves state-of-the-art accuracy.Comment: Accepted in the International Journal of Computer Vision (IJCV

Face recognition in the wild.

Research in face recognition deals with problems related to Age, Pose, Illumination and Expression (A-PIE), and seeks approaches that are invariant to these factors. Video images add a temporal aspect to the image acquisition process. Another degree of complexity, above and beyond A-PIE recognition, occurs when multiple pieces of information are known about people, which may be distorted, partially occluded, or disguised, and when the imaging conditions are totally unorthodox! A-PIE recognition in these circumstances becomes really “wild” and therefore, Face Recognition in the Wild has emerged as a field of research in the past few years. Its main purpose is to challenge constrained approaches of automatic face recognition, emulating some of the virtues of the Human Visual System (HVS) which is very tolerant to age, occlusion and distortions in the imaging process. HVS also integrates information about individuals and adds contexts together to recognize people within an activity or behavior. Machine vision has a very long road to emulate HVS, but face recognition in the wild, using the computer, is a road to perform face recognition in that path. In this thesis, Face Recognition in the Wild is defined as unconstrained face recognition under A-PIE+; the (+) connotes any alterations to the design scenario of the face recognition system. This thesis evaluates the Biometric Optical Surveillance System (BOSS) developed at the CVIP Lab, using low resolution imaging sensors. Specifically, the thesis tests the BOSS using cell phone cameras, and examines the potential of facial biometrics on smart portable devices like iPhone, iPads, and Tablets. For quantitative evaluation, the thesis focused on a specific testing scenario of BOSS software using iPhone 4 cell phones and a laptop. Testing was carried out indoor, at the CVIP Lab, using 21 subjects at distances of 5, 10 and 15 feet, with three poses, two expressions and two illumination levels. The three steps (detection, representation and matching) of the BOSS system were tested in this imaging scenario. False positives in facial detection increased with distances and with pose angles above ± 15°. The overall identification rate (face detection at confidence levels above 80%) also degraded with distances, pose, and expressions. The indoor lighting added challenges also, by inducing shadows which affected the image quality and the overall performance of the system. While this limited number of subjects and somewhat constrained imaging environment does not fully support a “wild” imaging scenario, it did provide a deep insight on the issues with automatic face recognition. The recognition rate curves demonstrate the limits of low-resolution cameras for face recognition at a distance (FRAD), yet it also provides a plausible defense for possible A-PIE face recognition on portable devices